The 58-year-old Koertzen beat the all-time record set by David Shepherd of England who stood in 172 one-day matches before retiring in 2005.
A member of the International Cricket Council (ICC) Elite Panel of umpires since 2002, Koertzen stood in the 1999 and 2003 World Cups.
The 2003 Cup semi-final between Australia and Sri Lanka in Port Elizabeth was his 100th one-dayer since making his international debut in a match between South Africa and India in Port Elizabeth in 1992.
Koertzen has also stood in 80 Tests.
ICC Umpires Manager Doug Cowie paid tribute to Koertzen's achievements.
"Rudis achievement is testament to his remarkable consistency and enormous ability as a decision-maker. He has proved himself to be unyielding, resilient, dependable, loyal and dedicated, all qualities that are needed to make it to the top of his profession," said Cowie, a former international umpire.
ICC President Percy Sonn, a countryman of Koertzen said: "For someone to stay at the top of his game for as long as Rudi has required incredible commitment and dedication. Thankfully, Rudi has that and his obvious love for what he does is apparent every time he takes the field."
"And on a personal note, as a South African its great to see him continue to do so well and we are all very proud of him at home."
Apart from Koertzen and Shepherd, West Indian Steve Bucknor (161), Australians Daryl Harper (141), Darrell Hair (131) and Simon Taufel (115), New Zealand's Billy Bowden (114), South Africa's David Orchard (107) and New Zealand's Steve Dunne (100) have stood in 100 or more one-dayers.